Ralf Grosse-Kunstleve has provided his SgLite module to enable PyMOL
to deduce symmetry relationships from standard space group and unit
cell information. Currently that information can only be provided to
PyMOL as a CRYST1 record in the PDB file, which includes the correct
space group identifier. However, it would be only a minor development
task to add a means of assigning unit-cell and symmetry to any molecule
object directly from the API.

When you use the "load" command to read in a PDB file with symmetry
information, matrix information should be output. Verify that this
information is produced before attempting to display symmetry related
molecules.

The "symexp" command is used to display symmetry related molecules in
the crystal lattice about an atom selection. This commands creates a
set of new objects with a common prefix. Each object in the series
corresponds to one symmetry-related object, which can be treated
independently. See "help symexp" or the reference section for usage
information.

In order to visualize only symmetry-related atoms within a given
distance, you need to break the process down into two steps. First, you
use the symexp command to create complete symmetry-related objects.
Then you use "hide" commands to restrict what is visible to only those
areas which you are interested.

The only map file format currently supported is the CNS and XPLOR
ASCII format map file. PyMOL can read large maps of this format and
then display arbitrary "bricks" of density within these maps about atom
selections.

Map objects are used to store the data and are represented by a
wire-frame brick in space indicating the extent of the map. An
arbitrary number of mesh or dots objects can be created from a given
map using the "isomesh" and "isodot" commands.

isomesh msh1,map1,1.0 # display an isosurface-mesh at level 1.0 over
# the entire map object "map1"
isomesh msh2,map1,1.0,(chain A),3.0 # display isosurface-mesh at 1.0
# in a brick about chain A with a
# border of 3.0 Angstroms

See "help isomesh" or the reference section for additional
information.